Variant report

Variant	rs9991405
Chromosome Location	chr4:158919854-158919855
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10022190	0.83[AFR][1000 genomes]
rs10461245	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461268	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10461269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13149552	0.86[AFR][1000 genomes]
rs28717075	0.86[AFR][1000 genomes]
rs35025809	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4389619	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457000	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9991405	TMEM144	cis	Esophagus Muscularis	GTEx
rs9991405	RP11-597D13.7	cis	Heart Left Ventricle	GTEx
rs9991405	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9991405	FAM198B	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158913800-158928200	Weak transcription	HSMM	muscle
2	chr4:158913800-158930000	Weak transcription	Right Atrium	heart
3	chr4:158914400-158923400	Weak transcription	Fetal Heart	heart
4	chr4:158915000-158924000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:158916400-158921400	Enhancers	HepG2	liver
6	chr4:158916400-158923000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:158917800-158922800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:158917800-158926400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:158918200-158923000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:158918800-158923000	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:158918800-158923000	Weak transcription	HUVEC	blood vessel
12	chr4:158919000-158922600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:158919800-158922200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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